Amber Archive Oct 2010 by thread
- [AMBER] runing mmpbsa.pl on cluster Giorgos Lamprinidis (Fri Oct 01 2010 - 01:58:54 PDT)
- [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Fri Oct 01 2010 - 03:04:57 PDT)
- Re: [AMBER] TI-Problems case (Fri Oct 01 2010 - 04:55:45 PDT)
- Re: [AMBER] spc/e water case (Fri Oct 01 2010 - 05:05:44 PDT)
- [AMBER] MMPBSA.py - very high energy terms Senthil Natesan (Fri Oct 01 2010 - 06:27:18 PDT)
- [AMBER] undefined reference in compiling amber10/gfortran Francesco Pietra (Fri Oct 01 2010 - 09:15:44 PDT)
- [AMBER] sander is running... nicholus bhattacharjee (Fri Oct 01 2010 - 09:41:43 PDT)
- Re: [AMBER] sander gb post-processing fail Trevor Gokey (Fri Oct 01 2010 - 12:11:23 PDT)
- Re: [AMBER] pmemd.cuda error with group restraint Ross Walker (Fri Oct 01 2010 - 16:59:30 PDT)
- [AMBER] sander.MPI error Sangita Kachhap (Sat Oct 02 2010 - 07:52:42 PDT)
- [AMBER] Segmentation fault Seibold, Stephen (Sat Oct 02 2010 - 14:33:41 PDT)
- [AMBER] mmpbsa.py error Anuradha Mittal (Sat Oct 02 2010 - 23:17:22 PDT)
- [AMBER] ptraj- cluster analysis - Error Senthil Natesan (Sun Oct 03 2010 - 10:15:01 PDT)
- [AMBER] MMPBSA Warning William Flak (Sun Oct 03 2010 - 11:12:47 PDT)
- [AMBER] Citations William Flak (Sun Oct 03 2010 - 16:16:12 PDT)
- [AMBER] Fwd: Amber installation Hadrian Djohari (Sun Oct 03 2010 - 22:30:39 PDT)
- [AMBER] Hydrogen Minimization and gradually relieving restraint on the DNA. abc def (Mon Oct 04 2010 - 00:11:38 PDT)
- [AMBER] mdcrd file subrata paul (Mon Oct 04 2010 - 04:04:22 PDT)
- [AMBER] make.parallel test got stuck !! any updates? Senthil Natesan (Mon Oct 04 2010 - 06:25:40 PDT)
- [AMBER] nmode Problem Dima A Sabbah (Mon Oct 04 2010 - 06:51:35 PDT)
- Re: [AMBER] NMR refinement in explicite water Baptiste Legrand (Mon Oct 04 2010 - 07:13:50 PDT)
- [AMBER] Potential Energy calculation in AMBER force field Ilyas Yildirim (Mon Oct 04 2010 - 12:34:37 PDT)
- [AMBER] Water bridge - MMPBSA William Flak (Mon Oct 04 2010 - 15:25:09 PDT)
- [AMBER] Water bridges Lekpa Duukori (Mon Oct 04 2010 - 15:34:18 PDT)
- [AMBER] Query regarding RMSD calculcation hirdesh kumar (Mon Oct 04 2010 - 22:51:22 PDT)
- [AMBER] TI +- variance is coming out to be very high sunita gupta (Tue Oct 05 2010 - 00:17:20 PDT)
- [AMBER] Query regarding solvent accessible surface area of individual residue hirdesh kumar (Tue Oct 05 2010 - 01:49:57 PDT)
- [AMBER] Sugars flexibility vs ionic strength Sergey Samsonov (Tue Oct 05 2010 - 03:00:13 PDT)
- [AMBER] unexpected numnghbr array William Flak (Tue Oct 05 2010 - 07:17:33 PDT)
- [AMBER] MMBPSA residue selection Federica Chiappori (Tue Oct 05 2010 - 08:01:05 PDT)
- [AMBER] nmode problem Sabbah, Dima (Tue Oct 05 2010 - 09:02:12 PDT)
- [AMBER] no nuclear spin in PIMD? aapeters.ncsu.edu (Tue Oct 05 2010 - 09:19:00 PDT)
- Re: [AMBER] PIMD average trajectory aapeters.ncsu.edu (Tue Oct 05 2010 - 12:58:08 PDT)
- [AMBER] how to stop printing restrt file in AMBER 11 Dian Jiao (Tue Oct 05 2010 - 16:31:45 PDT)
- [AMBER] mmpbsa error Anuradha Mittal (Tue Oct 05 2010 - 17:06:49 PDT)
- [AMBER] charges in prmtop file amit dong (Tue Oct 05 2010 - 18:34:01 PDT)
- [AMBER] intra-molecular energies of a water molecule Dian Jiao (Wed Oct 06 2010 - 00:11:53 PDT)
- [AMBER] TI problem - Antechamber changes the atom order FCUP (Wed Oct 06 2010 - 03:34:10 PDT)
- [AMBER] TI - vacuum problems FCUP (Wed Oct 06 2010 - 03:45:55 PDT)
- [AMBER] DNA and igb=2, igb=5 Ali M. Naserian-Nik (Wed Oct 06 2010 - 04:22:35 PDT)
- [AMBER] Protocol for structure determination of DNA duplex by NMR Olivier Julien (Wed Oct 06 2010 - 10:53:23 PDT)
- [AMBER] generating restraints Jorgen Simonsen (Wed Oct 06 2010 - 11:10:36 PDT)
- [AMBER] Ptraj Error- Analysis on Trajectory files Ajay Ummat (Wed Oct 06 2010 - 11:45:44 PDT)
- [AMBER] nab function transformmol() returned value docs are inconsistent M. L. Dodson (Wed Oct 06 2010 - 11:58:12 PDT)
- [AMBER] Stability problem shweta (Wed Oct 06 2010 - 18:56:18 PDT)
- [AMBER] RMSD doubt Soumya Lipsa Rath (Thu Oct 07 2010 - 00:49:22 PDT)
- [AMBER] maximum coordination exceeded $ set pert true William Flak (Thu Oct 07 2010 - 06:58:38 PDT)
- [AMBER] phosphorylated residues priyanka (Thu Oct 07 2010 - 09:43:20 PDT)
- [AMBER] Question about limitations of the nudged elastic band method patrick wintrode (Thu Oct 07 2010 - 17:43:22 PDT)
- [AMBER] ptraj mask Tyler Glembo (Thu Oct 07 2010 - 22:50:00 PDT)
- [AMBER] installation of pmemd fancy2012 (Fri Oct 08 2010 - 01:25:08 PDT)
- [AMBER] fix the positions of EP William Flak (Fri Oct 08 2010 - 07:56:50 PDT)
- Re: [AMBER] Pressure in bar or atm? Ben Roberts (Fri Oct 08 2010 - 08:34:36 PDT)
- [AMBER] Searching for a keyword William Flak (Fri Oct 08 2010 - 14:27:17 PDT)
- [AMBER] tutorials of TMD and REMD fancy2012 (Fri Oct 08 2010 - 20:15:31 PDT)
- [AMBER] V-limit exceeded in replica-exchang MD Cheng-I Lee (Fri Oct 08 2010 - 21:50:56 PDT)
- [AMBER] prepare the heme parameters juan zeng (Sat Oct 09 2010 - 00:18:08 PDT)
- [AMBER] Phosphorylated aspartate residue Rahul Banerjee (Sat Oct 09 2010 - 07:13:10 PDT)
- [AMBER] ptraj closest command William Flak (Sat Oct 09 2010 - 08:44:17 PDT)
- [AMBER] ligand geometry after simulation Computational Chemist (Sat Oct 09 2010 - 12:59:59 PDT)
- [AMBER] trajectory and topology file format Sangita Kachhap (Sun Oct 10 2010 - 06:49:08 PDT)
- [AMBER] restraint between two centers of mass? Jose Borreguero (Sun Oct 10 2010 - 07:35:44 PDT)
- [AMBER] partition error in shake xuemeiwang1103 (Sun Oct 10 2010 - 20:20:17 PDT)
- [AMBER] Ptraj LES split problem Bradshaw, Richard (Mon Oct 11 2010 - 05:08:35 PDT)
- [AMBER] remap umbrella sampling free-energy Giuseppe De Marco (Mon Oct 11 2010 - 10:57:22 PDT)
- Re: [AMBER] Shake errors Justine Shaw (Mon Oct 11 2010 - 12:43:01 PDT)
- [AMBER] xleap Siavoush Dastmalchi (Mon Oct 11 2010 - 21:54:48 PDT)
- [AMBER] error in atomic charge calculation in RED server Chinh Su Tran To (Mon Oct 11 2010 - 22:19:34 PDT)
- [AMBER] proton spin effects with Semi-empirical or DFTB qm/mm? aapeters.ncsu.edu (Tue Oct 12 2010 - 12:59:56 PDT)
- [AMBER] cz atom type Balazs Jojart (Tue Oct 12 2010 - 13:10:38 PDT)
- [AMBER] Solvate water moleculer in a TIP3PBOX oscarjiao.gmail.com (Tue Oct 12 2010 - 13:59:32 PDT)
- [AMBER] limitation of the protein size Cheng-I Lee (Tue Oct 12 2010 - 20:44:42 PDT)
- [AMBER] Normal mode analysis with QM potential 전종구 (Tue Oct 12 2010 - 22:52:22 PDT)
- [AMBER] ptraj box information Dickson, Callum (Wed Oct 13 2010 - 03:15:50 PDT)
- [AMBER] Water box deformed after heating step xue wang (Wed Oct 13 2010 - 07:09:41 PDT)
- [AMBER] new_type_solvent lara lara (Wed Oct 13 2010 - 09:00:15 PDT)
- [AMBER] new_solvent_type lara lara (Wed Oct 13 2010 - 09:23:53 PDT)
- [AMBER] Amber heme parameters Nitu Bansal (Wed Oct 13 2010 - 10:16:02 PDT)
- [AMBER] output pairwise energies Dian Jiao (Wed Oct 13 2010 - 10:25:04 PDT)
- [AMBER] xleap: SegFault on loadpdb Maura Catherine Mooney (Wed Oct 13 2010 - 10:41:40 PDT)
- [AMBER] restart file error shweta (Wed Oct 13 2010 - 10:57:43 PDT)
- [AMBER] MMPBSA protein-protein interaction Lars Skjærven (Thu Oct 14 2010 - 02:59:23 PDT)
- [AMBER] Issue regarding buckling of planar ligand during simulations abc def (Thu Oct 14 2010 - 04:43:31 PDT)
- [AMBER] antechamber error when processing the graphite structure Bongkeun Kim (Thu Oct 14 2010 - 13:02:13 PDT)
- [AMBER] About RMSD calculations hong-bin Xie (Thu Oct 14 2010 - 16:47:43 PDT)
- [AMBER] memory issue- CPHF- gamess calculation kamlesh sahu (Thu Oct 14 2010 - 18:24:35 PDT)
- [AMBER] Is it a typo in TUTORIAL A13: Simulation of a protein crystal? Ye MEI (Thu Oct 14 2010 - 21:05:25 PDT)
- [AMBER] build starting structure with >250 residues Cheng-I Lee (Thu Oct 14 2010 - 22:13:13 PDT)
- [AMBER] solvent_box_type lara lara (Thu Oct 14 2010 - 23:24:35 PDT)
- [AMBER] a question about replica-exchange MD Cheng-I Lee (Thu Oct 14 2010 - 23:24:32 PDT)
- [AMBER] mm_pbsa dependence on GB 0 or GB 1 Antonija Tomić (Fri Oct 15 2010 - 08:14:11 PDT)
- [AMBER] AMBER parallel version ying yu (Fri Oct 15 2010 - 21:40:31 PDT)
- [AMBER] binding free energy difference between PBTOT and GBTOT xue wang (Sun Oct 17 2010 - 07:07:39 PDT)
- [AMBER] mm-pbsa yan zhang (Sun Oct 17 2010 - 07:19:21 PDT)
- [AMBER] question on antechamber parametrization / unable to find mopac charges error Andrew Voronkov (Sun Oct 17 2010 - 10:35:07 PDT)
- [AMBER] PMEMD terminated abnormally! Ashutosh Shandilya (Mon Oct 18 2010 - 00:12:11 PDT)
- [AMBER] amber84 ASH parameters Francesco Pietra (Mon Oct 18 2010 - 00:59:15 PDT)
- [AMBER] solvent_shell_minimization_error balaji nagarajan (Mon Oct 18 2010 - 01:28:40 PDT)
- [AMBER] Output problem on Amber 9 Seren Soner (Mon Oct 18 2010 - 02:16:44 PDT)
- [AMBER] Problem with formyl group parameters Carter M.K. (Mon Oct 18 2010 - 03:36:44 PDT)
- [AMBER] residence time of water molecule and life time of hydrogen bonds atila petrosian (Mon Oct 18 2010 - 03:45:20 PDT)
- [AMBER] Parameters for succinimide Stephan Jakobi (Mon Oct 18 2010 - 05:17:57 PDT)
- [AMBER] QMMM: Unable to achieve self consistency to the tolerances specified sunita gupta (Mon Oct 18 2010 - 05:20:19 PDT)
- [AMBER] binding affinity calculation Sangita Kachhap (Mon Oct 18 2010 - 05:34:45 PDT)
- [AMBER] The result of entropy calculation DeChang Li (Mon Oct 18 2010 - 07:44:58 PDT)
- [AMBER] sphere_problem balaji nagarajan (Mon Oct 18 2010 - 09:19:12 PDT)
- Re: [AMBER] NMR_ensemble Raman Parkesh (Mon Oct 18 2010 - 15:20:41 PDT)
- [AMBER] interaction_energy balaji nagarajan (Mon Oct 18 2010 - 20:13:49 PDT)
- [AMBER] nmode calculation rameshwar prajapati (Tue Oct 19 2010 - 00:22:11 PDT)
- [AMBER] Mimiciking infinite DNA abc def (Tue Oct 19 2010 - 02:15:03 PDT)
- [AMBER] amb2gmx.pl script ignores negative values of PK? Andrei Neamtu (Tue Oct 19 2010 - 05:27:02 PDT)
- [AMBER] Umbrella sampling with temperature and pressure coupling method problem DeChang Li (Tue Oct 19 2010 - 05:57:33 PDT)
- [AMBER] magnesium ion parametrization question Andrew Voronkov (Tue Oct 19 2010 - 07:12:33 PDT)
- [AMBER] H-Bonding Beale, John (Tue Oct 19 2010 - 09:15:20 PDT)
- [AMBER] xmin fails with error in load_lbfgs() Don.Bashford.stjude.org (Tue Oct 19 2010 - 12:53:04 PDT)
- [AMBER] Amber10 build/installation problems Yazlovitsky, Boris (Tue Oct 19 2010 - 16:04:16 PDT)
- [AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Tue Oct 19 2010 - 22:24:19 PDT)
- [AMBER] Problem in mm_pbsa Kshatresh Dutta Dubey (Wed Oct 20 2010 - 00:00:54 PDT)
- [AMBER] calculate free energies using TI João Sardinha (Wed Oct 20 2010 - 04:01:55 PDT)
- Re: [AMBER] Residue not recognized case (Wed Oct 20 2010 - 06:45:11 PDT)
- [AMBER] residence time of water molecule and life time of hydrogen bonds atila petrosian (Wed Oct 20 2010 - 07:19:19 PDT)
- [AMBER] Can not addions with AMOEBA ff Igor Sizov (Wed Oct 20 2010 - 10:14:39 PDT)
- [AMBER] NMR-restrained RNA structure refinement with amber Michael F. Summers (Wed Oct 20 2010 - 11:03:09 PDT)
- [AMBER] pmemd 11 (parallel) compilation error - revisiting Alok Juneja (Wed Oct 20 2010 - 12:41:55 PDT)
- [AMBER] J-coupling restraints Mickey Richards (Wed Oct 20 2010 - 19:12:03 PDT)
- [AMBER] ncsu input eduardo.troche.uvigo.es (Thu Oct 21 2010 - 08:22:05 PDT)
- [AMBER] Infinite covalently bonded crystals Andrew Jewett (Thu Oct 21 2010 - 17:31:58 PDT)
- [AMBER] E(QM), E(MM), and E(QM/MM) components of the potential energy in sander output Dmitry Nilov (Fri Oct 22 2010 - 05:27:48 PDT)
- [AMBER] Triclinic box condition for PBC Bongkeun Kim (Fri Oct 22 2010 - 10:39:04 PDT)
- [AMBER] MMPBSA in AMBER11 zhihong ke (Fri Oct 22 2010 - 12:42:39 PDT)
- [AMBER] Measure relative orientations in amber 9 Neha Gandhi (Sat Oct 23 2010 - 01:38:22 PDT)
- [AMBER] Switching from NAMD to Amber for membrane Simulations Joshua Adelman (Sat Oct 23 2010 - 07:53:32 PDT)
- [AMBER] Nose Hoover thermostat Sangita Kachhap (Sat Oct 23 2010 - 11:43:21 PDT)
- [AMBER] about replica exchange Cheng-I Lee (Sun Oct 24 2010 - 17:01:08 PDT)
- [AMBER] pmemd installation error M. Reza Ganjalikhany (Mon Oct 25 2010 - 02:29:10 PDT)
- [AMBER] water molecule positions Beale, John (Mon Oct 25 2010 - 06:03:47 PDT)
- [AMBER] UREABOX tleap Michela Candotti (Mon Oct 25 2010 - 08:01:56 PDT)
- Re: [AMBER] Aromatic C and N atom type problems in Antechamber Gabriel Rocklin (Mon Oct 25 2010 - 15:21:00 PDT)
- [AMBER] Can we run sanders on GPU ? setyanto md (Mon Oct 25 2010 - 22:24:32 PDT)
- [AMBER] about Error while mapping in energy decomposition (Amber 10) Liane Saiz Urra (Tue Oct 26 2010 - 02:42:44 PDT)
- [AMBER] HOW TO PREPARE MODIFIED NUCLEOSIDE Indrajit Deb (Tue Oct 26 2010 - 05:11:07 PDT)
- [AMBER] Trajectory Minimization John S (Tue Oct 26 2010 - 06:57:23 PDT)
- [AMBER] Removing rotational motion John S (Tue Oct 26 2010 - 07:08:00 PDT)
- [AMBER] How to get the PDB file? xuemeiwang1103 (Tue Oct 26 2010 - 18:24:24 PDT)
- [AMBER] sidechain side chain interaction within one protein Rilei Yu (Tue Oct 26 2010 - 21:30:19 PDT)
- [AMBER] radial distibution function subrata paul (Tue Oct 26 2010 - 21:41:05 PDT)
- [AMBER] cannot generate snapshot_statistics.in file bin wang (Wed Oct 27 2010 - 08:52:49 PDT)
- [AMBER] Trajectory John S (Wed Oct 27 2010 - 10:15:23 PDT)
- [AMBER] Time-average restraint question Mickey Richards (Wed Oct 27 2010 - 11:03:37 PDT)
- [AMBER] 1D-RISM in NAB: compressibility units Andrej Frolov (Thu Oct 28 2010 - 00:52:26 PDT)
- [AMBER] free energy landscape fancy2012 (Thu Oct 28 2010 - 01:11:42 PDT)
- [AMBER] 3D-RISM in NAB: solvent susceptibility function support Andrej Frolov (Thu Oct 28 2010 - 01:11:52 PDT)
- [AMBER] regarding 'ambpdb' command in amber tools 1.4 aneesh cna (Thu Oct 28 2010 - 03:33:51 PDT)
- [AMBER] sander termination for large [NaCl] concentration Santosh Mogurampelly (Thu Oct 28 2010 - 05:17:50 PDT)
- [AMBER] 2drms in ptraj Beale, John (Thu Oct 28 2010 - 06:03:37 PDT)
- [AMBER] Update of renamed "initial_traj" to"strip_mdcrd" for MMPBSA.py in AMBER 11 Manual. Rafi Ahmad (Thu Oct 28 2010 - 06:58:26 PDT)
- [AMBER] cyclic_peptide lara lara (Thu Oct 28 2010 - 08:50:24 PDT)
- [AMBER] Protein Folding Jordan, Brad (Thu Oct 28 2010 - 11:25:40 PDT)
- [AMBER] Targeted MD Jordan, Brad (Thu Oct 28 2010 - 13:57:26 PDT)
- [AMBER] MMGBSA issue with covalently bound parameterized ligand Christopher Roberts (Thu Oct 28 2010 - 14:29:31 PDT)
- [AMBER] PARMSCAN Sarath Chandra Dantu (Fri Oct 29 2010 - 07:34:40 PDT)
- [AMBER] Error message from binding_energy.mmpbsa bin wang (Fri Oct 29 2010 - 07:50:19 PDT)
- [AMBER] extract distribution from PairwiseDistances Yannick SPILL (Fri Oct 29 2010 - 07:57:18 PDT)
- [AMBER] Targeted MD - minimization problem Jordan, Brad (Fri Oct 29 2010 - 09:33:51 PDT)
- [AMBER] Running NAB Arun Gupta (Fri Oct 29 2010 - 12:56:47 PDT)
- [AMBER] Stitching amino acid templates- sequence command tanya singh (Sat Oct 30 2010 - 08:51:42 PDT)
- [AMBER] GPU high temperature unfolding simulation andy ng (Sat Oct 30 2010 - 20:30:36 PDT)
- [AMBER] MMPBSA ligand/receptor selections Logan Ahlstrom (Sun Oct 31 2010 - 15:14:20 PDT)
- [AMBER] SCC-DFT orbitals arikcohen (Sun Oct 31 2010 - 22:24:38 PDT)
- Last message date: Sun Oct 31 2010 - 22:30:03 PDT
- Archived on: Sun Dec 22 2024 - 05:54:10 PST
